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Journal articles on the topic 'Diaminopimelate epimerase'

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Published: 10 December 2022

Last updated: 29 January 2023

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1

Miura, Hiromi, Kentaro Hori, Yosuke Sasaki, Yuki Inahashi, Yasufumi Yagisawa, Nobuyuki Fujita, Satoshi Ōmura, and Yōko Takahashi. "Simple analytic method of diaminopimelate epimerase activity." Journal of Bioscience and Bioengineering 116, no. 2 (August 2013): 253–55. http://dx.doi.org/10.1016/j.jbiosc.2013.02.015.

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2

Usha, Veeraraghavan, Lynn G. Dover, David I. Roper, Klaus Fütterer, and Gurdyal S. Besra. "Structure of the diaminopimelate epimerase DapF fromMycobacterium tuberculosis." Acta Crystallographica Section D Biological Crystallography 65, no. 4 (March 19, 2009): 383–87. http://dx.doi.org/10.1107/s0907444909002522.

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3

Lam, L. K., L. D. Arnold, T. H. Kalantar, J. G. Kelland, P. M. Lane-Bell, M. M. Palcic, M. A. Pickard, and J. C. Vederas. "Analogs of diaminopimelic acid as inhibitors of meso-diaminopimelate dehydrogenase and LL-diaminopimelate epimerase." Journal of Biological Chemistry 263, no. 24 (August 1988): 11814–19. http://dx.doi.org/10.1016/s0021-9258(18)37858-x.

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4

Stenta, Marco, Matteo Calvaresi, Piero Altoè, Domenico Spinelli, Marco Garavelli, Roberta Galeazzi, and Andrea Bottoni. "Catalytic Mechanism of Diaminopimelate Epimerase: A QM/MM Investigation." Journal of Chemical Theory and Computation 5, no. 7 (May 27, 2009): 1915–30. http://dx.doi.org/10.1021/ct900004x.

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5

Hor, Lilian, Renwick C. J. Dobson, Matthew T. Downton, John Wagner, Craig A. Hutton, and Matthew A. Perugini. "Dimerization of Bacterial Diaminopimelate Epimerase Is Essential for Catalysis." Journal of Biological Chemistry 288, no. 13 (February 19, 2013): 9238–48. http://dx.doi.org/10.1074/jbc.m113.450148.

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6

BARTLETT, A. T. M., and P. J. WHITE. "Species of Bacillus That Make a Vegetative Peptidoglycan Containing Lysine Lack Diaminopimelate Epimerase but Have Diaminopimelate Dehydrogenase." Microbiology 131, no. 9 (September 1, 1985): 2145–52. http://dx.doi.org/10.1099/00221287-131-9-2145.

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7

Hor, Lilian, Renwick C. J. Dobson, Con Dogovski, Craig A. Hutton, and Matthew A. Perugini. "Crystallization and preliminary X-ray diffraction analysis of diaminopimelate epimerase fromEscherichia coli." Acta Crystallographica Section F Structural Biology and Crystallization Communications 66, no. 1 (December 25, 2009): 37–40. http://dx.doi.org/10.1107/s1744309109047708.

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8

Pillai, B., M. M. Cherney, C. M. Diaper, A. Sutherland, J. S. Blanchard, J. C. Vederas, and M. N. G. James. "Structural insights into stereochemical inversion by diaminopimelate epimerase: An antibacterial drug target." Proceedings of the National Academy of Sciences 103, no. 23 (May 24, 2006): 8668–73. http://dx.doi.org/10.1073/pnas.0602537103.

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9

Vederas, John C. "2005 Alfred Bader Award Lecture Diaminopimelate and lysine biosynthesis - An antimicrobial target in bacteria." Canadian Journal of Chemistry 84, no. 10 (October 1, 2006): 1197–207. http://dx.doi.org/10.1139/v06-072.

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The development of bacterial resistance to current antibiotic therapy has stimulated the search for novel antimicrobial agents. The essential peptidoglycan cell wall layer in bacteria is the site of action of many current drugs, such as β-lactams and vancomycin. It is also a target for a number of very potent bacterially produced antibiotic peptides, such as nisin A and lacticin 3147, both of which are highly posttranslationally modified lantibiotics that act by binding to lipid II, the peptidoglycan precursor. Another set of potential targets for antibiotic development are the bacterial enzymes that make precursors for lipid II and peptidoglycan, for example, those in the pathway to diamino pimelic acid (DAP) and its metabolic product, L-lysine. Among these, DAP epimerase is a unique nonpyridoxal phosphate (PLP) dependent enzyme that appears to use two active site thiols (Cys73 and Cys217) as a base and an acid to depro tonate the α-hydrogen of LL-DAP or meso-DAP from one side and reprotonate from the other. This process cannot be easily duplicated in the absence of the enzyme. A primary goal of our work was to generate inhibitors of DAP epi merase that would accurately mimic the natural substrates (meso-DAP and LL-DAP) in the enzyme active site and, through crystallographic analysis, provide insight into mechanism and substrate specificity. A series of aziridine-containing DAP analogs were chemically synthesized and tested as inhibitors of DAP epimerase from Haemophilus influenzae. Two diastereomers of 2-(4-amino-4-carboxybutyl)aziridine-2-carboxylic acid (AziDAP) act as rapid irreversible inactivators of DAP epimerase; the AziDAP analog of LL-DAP reacts selectively with the sulfhydryl of Cys73, whereas the corresponding analog of meso-DAP reacts with Cys217. AziDAP isomers are too unstable to be useful antibiotics. However, mass spectral and X-ray crystallographic analyses of the inactivated enzymes confirm that the thiol attacks the methylene group of the aziridine with concomitant ring opening to give a DAP analog bound in the active site. Further crystallographic analyses should yield useful mechanistic insights.Key words: enzyme mechanism, enzyme inhibition, antibiotics, aziridines, amino acids.

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10

Park, Jeong Soon, Woo Cheol Lee, Jung Hyun Song, Seung Il Kim, Je Chul Lee, Chaejoon Cheong, and Hye-Yeon Kim. "Purification, crystallization and preliminary X-ray crystallographic analysis of diaminopimelate epimerase fromAcinetobacter baumannii." Acta Crystallographica Section F Structural Biology and Crystallization Communications 69, no. 1 (December 20, 2012): 42–44. http://dx.doi.org/10.1107/s1744309112048506.

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11

Koo, Carolyn W., Andrew Sutherland, John C. Vederas, and John S. Blanchard. "Identification of Active Site Cysteine Residues that Function as General Bases: Diaminopimelate Epimerase." Journal of the American Chemical Society 122, no. 25 (June 2000): 6122–23. http://dx.doi.org/10.1021/ja001193t.

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12

Pillai, Bindu, Maia Cherney, Christopher M. Diaper, Andrew Sutherland, John S. Blanchard, John C. Vederas, and Michael N. G. James. "Dynamics of catalysis revealed from the crystal structures of mutants of diaminopimelate epimerase." Biochemical and Biophysical Research Communications 363, no. 3 (November 2007): 547–53. http://dx.doi.org/10.1016/j.bbrc.2007.09.012.

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13

Brunetti, L., R. Galeazzi, M. Orena, and A. Bottoni. "Catalytic mechanism of l,l-diaminopimelic acid with diaminopimelate epimerase by molecular docking simulations." Journal of Molecular Graphics and Modelling 26, no. 7 (April 2008): 1082–90. http://dx.doi.org/10.1016/j.jmgm.2007.09.005.

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14

Grassick, Alice, Gerlind Sulzenbacher, Véronique Roig-Zamboni, Valérie Campanacci, Christian Cambillau, and Yves Bourne. "Crystal structure of E. coli yddE protein reveals a striking homology with diaminopimelate epimerase." Proteins: Structure, Function, and Bioinformatics 55, no. 3 (April 1, 2004): 764–67. http://dx.doi.org/10.1002/prot.20025.

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15

HIGGINS, William, Chantal TARDIF, Catherine RICHAUD, Michele A. KRIVANEK, and Alan CARDIN. "Expression of recombinant diaminopimelate epimerase in Escherichia coli. Isolation and inhibition with an irreversible inhibitor." European Journal of Biochemistry 186, no. 1-2 (December 1989): 137–43. http://dx.doi.org/10.1111/j.1432-1033.1989.tb15187.x.

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16

Richaud, C., W. Higgins, D. Mengin-Lecreulx, and P. Stragier. "Molecular cloning, characterization, and chromosomal localization of dapF, the Escherichia coli gene for diaminopimelate epimerase." Journal of Bacteriology 169, no. 4 (1987): 1454–59. http://dx.doi.org/10.1128/jb.169.4.1454-1459.1987.

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17

Weir, A. N. C., C. Bucke, G. Holt, M. D. Lilly, and A. T. Bull. "A high-performance liquid chromatography method for the simultaneous assay of diaminopimelate epimerase and decarboxylase." Analytical Biochemistry 180, no. 2 (August 1989): 298–302. http://dx.doi.org/10.1016/0003-2697(89)90434-x.

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18

Mengin-Lecreulx, D., C. Michaud, C. Richaud, D. Blanot, and J. van Heijenoort. "Incorporation of LL-diaminopimelic acid into peptidoglycan of Escherichia coli mutants lacking diaminopimelate epimerase encoded by dapF." Journal of Bacteriology 170, no. 5 (1988): 2031–39. http://dx.doi.org/10.1128/jb.170.5.2031-2039.1988.

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19

Gelb, Michael H., Yukang Lin, Michael A. Pickard, Yonghong Song, and John C. Vederas. "Synthesis of 3-fluorodiaminopimelic acid isomers as inhibitors of diaminopimelate epimerase: stereocontrolled enzymatic elimination of hydrogen fluoride." Journal of the American Chemical Society 112, no. 12 (June 1990): 4932–42. http://dx.doi.org/10.1021/ja00168a045.

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20

Pillai, Bindu, Vijayalakshmi A. Moorthie, Marco J. van Belkum, Sandra L. Marcus, Maia M. Cherney, Christopher M. Diaper, John C. Vederas, and Michael N. G. James. "Crystal Structure of Diaminopimelate Epimerase from Arabidopsis thaliana, an Amino Acid Racemase Critical for l-Lysine Biosynthesis." Journal of Molecular Biology 385, no. 2 (January 2009): 580–94. http://dx.doi.org/10.1016/j.jmb.2008.10.072.

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21

Kumagai, Takanori, Yusuke Koyama, Kosuke Oda, Masafumi Noda, Yasuyuki Matoba, and Masanori Sugiyama. "Molecular Cloning and Heterologous Expression of a Biosynthetic Gene Cluster for the Antitubercular Agent d-Cycloserine Produced by Streptomyces lavendulae." Antimicrobial Agents and Chemotherapy 54, no. 3 (January 19, 2010): 1132–39. http://dx.doi.org/10.1128/aac.01226-09.

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ABSTRACT In the present study, we successfully cloned a 21-kb DNA fragment containing a d-cycloserine (DCS) biosynthetic gene cluster from a DCS-producing Streptomyces lavendulae strain, ATCC 11924. The putative gene cluster consists of 10 open reading frames (ORFs), designated dcsA to dcsJ. This cluster includes two ORFs encoding d-alanyl-d-alanine ligase (dcsI) and a putative membrane protein (dcsJ) as the self-resistance determinants of the producer organism, indicated by our previous work. When the 10 ORFs were introduced into DCS-nonproducing Streptomyces lividans 66 as a heterologous host cell, the transformant acquired DCS productivity. This reveals that the introduced genes are responsible for the biosynthesis of DCS. As anticipated, the disruption of dcsG, seen in the DCS biosynthetic gene cluster, made it possible for the strain ATCC 11924 to lose its DCS production. We here propose the DCS biosynthetic pathway. First, l-serine is O acetylated by a dcsE-encoded enzyme homologous to homoserine O-acetyltransferase. Second, O-acetyl-l-serine accepts hydroxyurea via an O-acetylserine sulfhydrylase homolog (dcsD product) and forms O-ureido-l-serine. The hydroxyurea must be supplied by the catalysis of a dcsB-encoded arginase homolog using the l-arginine derivative, N G-hydroxy-l-arginine. The resulting O-ureido-l-serine is then racemized to O-ureido-d-serine by a homolog of diaminopimelate epimerase. Finally, O-ureido-d-serine is cyclized to form DCS with the release of ammonia and carbon dioxide. The cyclization must be done by the dcsG or dcsH product, which belongs to the ATP-grasp fold family of protein.

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22

Uda, Narutoshi, Yasuyuki Matoba, Takanori Kumagai, Kosuke Oda, Masafumi Noda, and Masanori Sugiyama. "Establishment of anIn Vitrod-Cycloserine-Synthesizing System by UsingO-Ureido-l-Serine Synthase and d-Cycloserine Synthetase Found in the Biosynthetic Pathway." Antimicrobial Agents and Chemotherapy 57, no. 6 (March 25, 2013): 2603–12. http://dx.doi.org/10.1128/aac.02291-12.

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ABSTRACTWe have recently cloned a DNA fragment containing a gene cluster that is responsible for the biosynthesis of an antituberculosis antibiotic,d-cycloserine. The gene cluster is composed of 10 open reading frames, designateddcsAtodcsJ. Judging from the sequence similarity between each putative gene product and known proteins, DcsC, which displays high homology to diaminopimelate epimerase, may catalyze the racemization ofO-ureidoserine. DcsD is similar toO-acetylserine sulfhydrylase, which generatesl-cysteine usingO-acetyl-l-serine with sulfide, and therefore, DcsD may be a synthase to generateO-ureido-l-serine usingO-acetyl-l-serine and hydroxyurea. DcsG, which exhibits similarity to a family of enzymes with an ATP-grasp fold, may be an ATP-dependent synthetase convertingO-ureido-d-serine intod-cycloserine. In the present study, to characterize the enzymatic functions of DcsC, DcsD, and DcsG, each protein was overexpressed inEscherichia coliand purified to near homogeneity. The biochemical function of each of the reactions catalyzed by these three proteins was verified by thin-layer chromatography (TLC), high-performance liquid chromatography (HPLC), and, in some cases, mass spectrometry. The results from this study demonstrate that by using a mixture of the three purified enzymes and the two commercially available substratesO-acetyl-l-serine and hydroxyurea, synthesis ofd-cycloserine was successfully attained. Thesein vitrostudies yield the conclusion that DcsD and DcsG are necessary for the syntheses ofO-ureido-l-serine andd-cycloserine, respectively. DcsD was also able to catalyze the synthesis ofl-cysteine when sulfide was added instead of hydroxyurea. Furthermore, the present study shows that DcsG can also form other cyclicd-amino acid analogs, such asd-homocysteine thiolactone.

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23

Williams, Robert M., Glenn J. Fegley, Reneé Gallegos, Felicity Schaefer, and David L. Pruess. "Asymmetric Syntheses of (2S,3S,6S)-, (2S,3S,6R)-, and (2R,3R,6S)-2,3-Methano-2,6-diaminopimelic Acids. Studies Directed to the Design of Novel Substrate-based Inhibitors of L,L-Diaminopimelate Epimerase." Tetrahedron 52, no. 4 (January 1996): 1149–64. http://dx.doi.org/10.1016/0040-4020(95)00976-0.

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24

WILLIAMS, R. M., G. J. FEGLEY, R. GALLEGOS, F. SCHAEFER, and D. L. PRUESS. "ChemInform Abstract: Asymmetric Syntheses of (2S,3S,6S)-(X), (2S,3S,6R)-, and (2R,3R,6S)-2, 3-Methano-2,6-diaminopimelic Acids. Studies Directed to the Design of Novel Substrate-Based Inhibitors of L,L-Diaminopimelate (DAP) Epimerase." ChemInform 27, no. 19 (August 5, 2010): no. http://dx.doi.org/10.1002/chin.199619230.

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25

Liechti, George, Raghuveer Singh, Patricia L. Rossi, Miranda D. Gray, Nancy E. Adams, and Anthony T. Maurelli. "Chlamydia trachomatis dapFEncodes a Bifunctional Enzyme Capable of Both D-Glutamate Racemase and Diaminopimelate Epimerase Activities." mBio 9, no. 2 (April 3, 2018). http://dx.doi.org/10.1128/mbio.00204-18.

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ABSTRACTPeptidoglycan is a sugar/amino acid polymer unique to bacteria and essential for division and cell shape maintenance. Thed-amino acids that make up its cross-linked stem peptides are not abundant in nature and must be synthesized by bacteriade novo.d-Glutamate is present at the second position of the pentapeptide stem and is strictly conserved in all bacterial species. In Gram-negative bacteria,d-glutamate is generated via the racemization ofl-glutamate by glutamate racemase (MurI).Chlamydia trachomatisis the leading cause of infectious blindness and sexually transmitted bacterial infections worldwide. While its genome encodes a majority of the enzymes involved in peptidoglycan synthesis, nomurIhomologue has ever been annotated. Recent studies have revealed the presence of peptidoglycan inC. trachomatisand confirmed that its pentapeptide includesd-glutamate. In this study, we show thatC. trachomatissynthesizesd-glutamate by utilizing a novel, bifunctional homologue of diaminopimelate epimerase (DapF). DapF catalyzes the final step in the synthesis ofmeso-diaminopimelate, another amino acid unique to peptidoglycan. Genetic complementation of anEscherichia coli murImutant demonstrated thatChlamydiaDapF can generated-glutamate. Biochemical analysis showed robust activity, but unlike canonical glutamate racemases, activity was dependent on the cofactor pyridoxal phosphate. Genetic complementation, enzymatic characterization, and bioinformatic analyses indicate that chlamydial DapF shares characteristics with other promiscuous/primordial enzymes, presenting a potential mechanism ford-glutamate synthesis not only inChlamydiabut also numerous other genera within thePlanctomycetes-Verrucomicrobiae-Chlamydiaesuperphylum that lack recognized glutamate racemases.IMPORTANCEHere we describe one of the last remaining “missing” steps in peptidoglycan synthesis in pathogenicChlamydiaspecies, the synthesis ofd-glutamate. We have determined that the diaminopimelate epimerase (DapF) encoded byChlamydia trachomatisis capable of carrying out both the epimerization of DAP and the pyridoxal phosphate-dependent racemization of glutamate. Enzyme promiscuity is thought to be the hallmark of early microbial life on this planet, and there is currently an active debate as to whether “moonlighting enzymes” represent primordial evolutionary relics or are a product of more recent reductionist evolutionary pressures. Given the large number ofChlamydiaspecies (as well as members of thePlanctomycetes-Verrucomicrobiae-Chlamydiaesuperphylum) that possess DapF but lack homologues of MurI, it is likely that DapF is a primordial isomerase that functions as both racemase and epimerase in these organisms, suggesting that specializedd-glutamate racemase enzymes never evolved in these microbes.

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26

Yamanaka, Kazuya, Ryo Ozaki, Yoshimitsu Hamano, and Tadao Oikawa. "Molecular and Mechanistic Characterization of PddB, the First PLP-Independent 2,4-Diaminobutyric Acid Racemase Discovered in an Actinobacterial D-Amino Acid Homopolymer Biosynthesis." Frontiers in Microbiology 12 (June 10, 2021). http://dx.doi.org/10.3389/fmicb.2021.686023.

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We recently disclosed that the biosynthesis of antiviral γ-poly-D-2,4-diaminobutyric acid (poly-D-Dab) in Streptoalloteichus hindustanus involves an unprecedented cofactor independent stereoinversion of Dab catalyzed by PddB, which shows weak homology to diaminopimelate epimerase (DapF). Enzymological properties and mechanistic details of this enzyme, however, had remained to be elucidated. Here, through a series of biochemical characterizations, structural modeling, and site-directed mutageneses, we fully illustrate the first Dab-specific PLP-independent racemase PddB and further provide an insight into its evolution. The activity of the recombinant PddB was shown to be optimal around pH 8.5, and its other fundamental properties resembled those of typical PLP-independent racemases/epimerases. The enzyme catalyzed Dab specific stereoinversion with a calculated equilibrium constant of nearly unity, demonstrating that the reaction catalyzed by PddB is indeed racemization. Its activity was inhibited upon incubation with sulfhydryl reagents, and the site-directed substitution of two putative catalytic Cys residues led to the abolishment of the activity. These observations provided critical evidence that PddB employs the thiolate-thiol pair to catalyze interconversion of Dab isomers. Despite the low levels of sequence similarity, a phylogenetic analysis of PddB indicated its particular relevance to DapF among PLP-independent racemases/epimerases. Secondary structure prediction and 3D structural modeling of PddB revealed its remarkable conformational analogy to DapF, which in turn allowed us to predict amino acid residues potentially responsible for the discrimination of structural difference between diaminopimelate and its specific substrate, Dab. Further, PddB homologs which seemed to be narrowly distributed only in actinobacterial kingdom were constantly encoded adjacent to the putative poly-D-Dab synthetase gene. These observations strongly suggested that PddB could have evolved from the primary metabolic DapF in order to organize the biosynthesis pathway for the particular secondary metabolite, poly-D-Dab. The present study is on the first molecular characterization of PLP-independent Dab racemase and provides insights that could contribute to further discovery of unprecedented PLP-independent racemases.

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27

Chaudhary, Jyoti, Nagendra Singh, Vijay Kumar Srivastava, Anupam Jyoti, and Sanket Kaushik. "Exploring the significance of diaminopimelate epimerase as a drug target in multidrug resistant Enterococcus faecalis." Vegetos, September 30, 2022. http://dx.doi.org/10.1007/s42535-022-00485-1.

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28

Singh, Harpreet, Satyajeet Das, Jyoti Yadav, Vijay Kumar Srivastava, Anupam Jyoti, and Sanket Kaushik. "In silico prediction, molecular docking and binding studies of acetaminophen and dexamethasone to Enterococcus faecalis diaminopimelate epimerase." Journal of Molecular Recognition 34, no. 9 (March 14, 2021). http://dx.doi.org/10.1002/jmr.2894.

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29

Sagong, Hye-Young, and Kyung-Jin Kim. "Structural basis for redox sensitivity in Corynebacterium glutamicum diaminopimelate epimerase: an enzyme involved in l-lysine biosynthesis." Scientific Reports 7, no. 1 (February 8, 2017). http://dx.doi.org/10.1038/srep42318.

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30

GELB, M. H., Y. LIN, M. A. PICKARD, Y. SONG, and J. C. VEDERAS. "ChemInform Abstract: Synthesis of 3-Fluorodiaminopimelic Acid Isomers as Inhibitors of Diaminopimelate Epimerase: Stereocontrolled Enzymatic Elimination of Hydrogen Fluoride." ChemInform 21, no. 40 (October 2, 1990). http://dx.doi.org/10.1002/chin.199040305.

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